BIOL 263: Molecular Biology and Genomics
MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall Room 101
(Owen York Lecture Hall)
Dr. Wade Powell
FSH 202, PBX 5396
Office hours: M 11 AM - noon and 3 - 4 PM; W, 11AM - 1 PM; F, 11AM - noon
(and by appointment)
The molecular and genomic basis of life is at the heart of modern biology. In BIOL 263, we will learn techniques and explore research questions at the forefront of molecular research, focusing on the mechanisms by which the information of the genome is expressed to form the functional molecules of living cells and organisms. The processes of DNA replication, recombination and repair, transcription of RNA from DNA templates, and translation of RNA into protein are discussed in the context of current research, frequently using primary literature. The function of genes and regulation and measurement of gene expression are treated in depth. Students analyze and publish interactive tutorials on the structure and function of key macromolecules. This intermediate-level course presumes a strong background in the basics of protein structure/function, central dogma processes, fundamental molecular techniques for manipulating nucleic acids and proteins, and general chemistry.
Required prerequisites: BIOL 113, 114; one year of chemistry; or permission of the instructor.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic Chemistry).
Reading Materials and Resources:
All reading assignments must be completed before class on the date indicated on syllabus.
Assignments and Grades: Your grade is based on performance in the following areas:
Part I: Molecular Interactions
|M||Aug 29||Course Introduction. DNA intro; 3D; B-DNA; A-RNA; DNA & RNA
|W||Aug 31||Weak bonds. Amino Acids; CAP; FAB; Ident||Watson Ch 3; Ch 5, pp. 69-73|
|F||Sept 2||Adv DNA. FT; Z-DNA ; HIV; Triplex; Quad; base tautomers; supercoiling; Topo||Watson Ch 6||Notes|
|M||Sept 5||AA2 in proteins.||Ch 5 p 73-92;||Notes|
|W||Sept 7||basic X-ray; more advanced X-Ray (local version); another explanation (pdf).||Notes|
|F||Sept 9||DNA-protein binding; Vocab; Human ADAR1;
ADAR activity and consequence
Reading journal articles.
Part II: Gene Expression
|M||Sept 12||Transcription initiation
Structures: RnaPol-Bact; RnaPol-Euk
|Watson Ch 12 pp. 347-363;||Notes|
|W||Sept 14||Transcription Elongation; transcriptional road blocks
Structures: RnaPol-Bact; RnaPol-Euk
|Epshtein & Nudler 2003|
|F||Sept 16||Watson Ch 16, pp. 483-504||Notes|
|M||Sept 19||Regulation of intiation, cont'd;
Regulation of events after initiation: Attenuation in E. coli.
|Watson Ch 16, pp.504-511;
|W||Sept 21||Attenuation in Bacillus. TRAP-RNA;
Transcriptional regulation without regulatory proteins: Riboswitches.
Watson Ch. 16, pp. 509-510; Soukup 2004
|F||Sept 23||Catch-up day
Remarks about Monday's exam.
Points to ponder for the exam.
|Breaker Lab Riboswitch site (Yale) & ppt movie||Notes|
|M||Sept 26||Exam I (in class)|
|W||Sept 28||Eukaryotic Basal Transcription Factors. DAB PolII; TBP; TAF
||Watson Ch. 12 pp.363-377;
Ch. 16, Box 16-1 (pp. 490-491).
|F||Sept 30||Eukaryotic Transcriptional Regulation; Spec. TFs. Activators; Identify
||Watson Ch, 17, pp. 529-555;||Notes|
|M||Oct 3||Eukaryotic Transcription, cont'd.||.||.|
|W||Oct 5||Nucleosomes & Transcriptional regulation; Histone Code. Figures; Nucleosome|| Watson Ch. 7 pp. 151-180; Ch. 17 p. 540 & pp. 556-562.
|F||Oct 7||Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment||Sharma 2002
|M||Oct 10||October Reading Days; No Class|
|W||Oct 12||Transcript Splicing; Lupus; Splicing2; Spliceosome||Watson Ch. 13||Notes|
|F||Oct 14||Translation initiation. Initiation. PDB||Watson Ch. 14, pp. 411-439.||Notes||PDB Proposal|
|M||Oct 17||Translation elongation, termination.||Watson Ch. 14. pp. 440-459.||Notes|
|W||Oct 19||Finish translation process;
"Protein Jive Sutra"
|Watson Ch. 14.|
|F||Oct 21||Translation in the Nucleus? Notes
|M||Oct 24||RNA Interference
Animation from Nature Reviews Genetics .
04 (RNAi review paper)
Watson Ch. 17 pp. 567-570
|W||Oct 26||Argonaute in RNAi||Liu 04
* supporting materials
|F||Oct 28||Exam II (points to ponder)|
Part III: DNA Replication, Repair, Recombination
|M||Oct 31||class cancelled|
|W||Nov 2||DNA Replication; Beta ring; DNA Rep; Replisome||Watson Ch. 8||Notes|
|F||Nov 4||DNA Rep., cont'd.;||Watson Ch. 8
|M||Nov 7||Mutation and repair.||Watson Ch. 9||Notes||Web Project Workshop 8-10 PM|
|W||Nov 9||MutS; MutS-DNA; Figs.||Obmolova 00||Web Project Workshop 8-10 PM|
|F||Nov 11||Recombination; Experiments; RuvA; PNAS; Tn;||Watson Ch. 10|
Part IV: Genomics
|M||Nov 14||Schulze 2001 review article
Watson Ch. 18, pp. 575-577
|W||Nov 16||Microarray Research: Diurnal & circadian related gene expression||Schaffer 2001||Supplemental material|
|F||Nov 18||Genomes: Human Genome; Ensembl
Black heart drug; Designer Babies
|Watson Ch. 2, p. 38-39; Ch. 7, p. 133-138; Ch. 20, p. 660-671.||Notes|
|Nov 19-27||Thanksgiving Break|
Part V: Hot Topics
|M||Nov 28||Telomerase and telomeres||Watson Ch. 8 p. 229-232.
Blackburn 2000 review
|Notes||Telomeres 12-mer; 22-mer|
|W||Nov 30||Telomerase depletion and cancer cell division||Li et al. 2005|
|F||Dec 2||Knockout mice in molecular biology|
|M||Dec 5||Exam Review|
|W||Dec 7||Exam III|
|F||Dec 9||Student Project Presentations||Completed Chime Tutorial|
|M||Dec 12||Student Project Presentations|
|Sat||Dec 17||Revised Chime Tutorials Due||No Broken Links||8:30 PM|